Camelia, the Perl 6 bug

IRC log for #cdk, 2012-04-03

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All times shown according to UTC.

Time Nick Message
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08:55 konditorn egonw: I've a patch that adds this new SINGLE_OR_DOUBLE-flag and do some simple tests of it. what do you want me to do with it?
08:58 konditorn mail it on the Cdk-devel-list?
09:19 egonw can you put it on GitHub?
09:20 konditorn as a pull-request?
09:21 egonw I will look at it first
09:22 egonw after that, you can file your patch here: http://sourceforge.net/tracker/​?group_id=20024&atid=320024
09:22 egonw no wait
09:22 egonw maybe we should make a branch of patches you and I are happy with first
09:24 konditorn I've made my changes in a branch I call "Aromaticity"… =)
09:25 egonw what's your github account?
09:26 konditorn KlasJoensson
09:28 egonw did you fork the CDK on GitHub? I cannot find it...
09:29 konditorn no..
09:30 konditorn now, I have forked it
09:31 egonw konditorn: http://apps.ideaconsult.net:8080/ambi​t2/depict/cdk?search=c2ccc3n%28%5BH%5​D%29c1ccccc1c3%28c2%29&smarts=a
09:32 konditorn yes…?
09:32 CIA-121 cdk: Egon Willighagen cdk-1.4.x * ra6597e3 / src/test/org/openscience/cdk/smil​es/DeduceBondSystemToolTest.java :
09:32 CIA-121 cdk: Added testing of the number of double bonds found (fixes #3514176)
09:32 CIA-121 cdk: Change-Id: I1d2740ce310a767c9fa236be5b602ac64ee9b5d9
09:32 CIA-121 cdk: Signed-off-by: ngn <jeliazkova.nina@gmail.com> - http://git.io/0pJTWw
09:32 CIA-121 cdk: Egon Willighagen cdk-1.4.x * rfb37eab / (2 files in 2 dirs):
09:32 CIA-121 cdk: Double bond orders are not properly assigned when using the SilentCOB
09:32 CIA-121 cdk: Change-Id: I299374c6ad0bf75f1e97ace99de52cb813e5c221
09:32 CIA-121 cdk: Signed-off-by: ngn <jeliazkova.nina@gmail.com> - http://git.io/jg0d7g
09:32 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r1e936d0 / src/main/org/openscience/cdk/sm​iles/DeduceBondSystemTool.java :
09:32 CIA-121 cdk: Fixed bond order assignment when using the SilentCOB
09:32 CIA-121 cdk: Change-Id: Ic6427e6399d645b600f5e6f1c0f438335cd91298
09:32 CIA-121 cdk: Signed-off-by: ngn <jeliazkova.nina@gmail.com> - http://git.io/fPuNmg
09:32 egonw konditorn: a debug tool :)
09:32 egonw here we can see what the current code does
09:32 konditorn oki =)
09:32 egonw nina just gave me this corner case: http://apps.ideaconsult.net:8080/ambit​2/depict/cdk?search=c1ccccc2ccccc3cccc​5ccccc6ccccc7cccccccc7ccccccc6cccccccc​5ccccc3ccccccc2cccccccc1&amp;smarts=a
09:34 konditorn looks to me as if its working...
09:34 egonw the SaturationChecker does a decent job
09:34 egonw this is a "classical" corner case for double bonding finding: http://apps.ideaconsult.net:8080/ambit​2/depict/cdk?search=cccc&amp;smarts=a
09:37 egonw the DBST does not work for that, because it works for rings
09:37 konditorn is it good or bad (sorry, my knowledge in chemistry isn't so good…)
09:38 konditorn ok, so the best guess should look like the top right image?
09:38 egonw in this case, yes
09:39 egonw I will try to dig up all the corner cases
09:39 egonw and add those to the GDoc
09:39 konditorn ok
09:42 egonw konditorn: and if you like to see what other cheminfo tools do, remove the "/cdk" part from the URL
09:44 konditorn they get the double-bond right...
09:45 egonw ah, you cloned 'my' cdk ...
09:45 egonw there is also:
09:45 egonw github.com/cdk/cdk
09:45 egonw :)
09:45 egonw you know how you can delete branches on GitHub?
09:45 egonw like all those development branches of mine :)
09:45 konditorn oki, I just took the one of the top of the results...
09:46 konditorn by using the "Unwatch" ?
09:47 egonw dunno if you can do it via the website, or how
09:47 egonw from the command line you can do:
09:47 egonw (assuming 'origin' is your GitHub fork)
09:48 egonw git push origin :355-m-mopacCharge
09:48 egonw the colon indicates the removal
09:52 konditorn the one that I have imported to my computer is from https://github.com/cdk/cdk.git
09:56 konditorn but the one that I forked on github today is https://github.com/egonw/cdk.git
09:59 konditorn so I guess that I shall remove the fork I did from your repo and make new fork from cdk…?
10:02 konditorn afk: suchi...
10:02 egonw good!
10:02 egonw I miss the sushi :(
10:05 egonw yeah, that is a good option
10:49 CIA-121 cdk: Egon Willighagen cdk-1.4.9 * re754060 / build.props :
10:49 CIA-121 cdk: Bumped version number to 1.4.9
10:49 CIA-121 cdk: Change-Id: I524b508f28a5ca6ee1a97dd4210c511fe1b40dbb - http://git.io/gQMAlw
10:49 CIA-121 cdk: Egon Willighagen cdk-1.4.x * re754060 / build.props :
10:49 CIA-121 cdk: Bumped version number to 1.4.9
10:49 CIA-121 cdk: Change-Id: I524b508f28a5ca6ee1a97dd4210c511fe1b40dbb - http://git.io/gQMAlw
10:49 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r364c9a4 / build.props :
10:49 CIA-121 cdk: Open for bug fixing
10:49 CIA-121 cdk: Change-Id: If0050db9e515a91feabb927b1dd091561e22f4c8 - http://git.io/fdDLsA
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14:29 slyrus egonw: where did that ambit drawing page come from? very nice!
14:29 slyrus are those CDK drawn structures?
14:30 egonw which of the two URL?
14:30 egonw depict/cdk? is all CDK
14:31 egonw depict? is four different tools, of which one is CDK
14:34 konditorn egonw: I've made an pull request to https://github.com/cdk/cdk.git, with my implementation of the new flag...
14:35 konditorn if you want me to mail it as patch to you (or any one else) just tell me. =)
14:58 egonw mail cdk-devel is ok, or file a patch in the Patch tracker on SF:
14:59 egonw http://sourceforge.net/tracker/​?group_id=20024&amp;atid=320024
15:08 slyrus egonw: this one http://apps.ideaconsult.net:8080/ambit​2/depict/cdk?search=c1ccccc2ccccc3cccc​5ccccc6ccccc7cccccccc7ccccccc6cccccccc​5ccccc3ccccccc2cccccccc1&amp;smarts=a
15:08 egonw yeah, that's all CDK
15:08 slyrus nice
15:09 slyrus the name ambit is overloaded...
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